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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-07-16, 16:51 based on data in: /work/users/p/r/prisca/antibiotics_tolerance/data/working/fastqc_initial


        General Statistics

        Showing 270/270 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        BMT101D-7_CTCTCTAC-TCTTACGC_S81_L004_R1_001
        57.9%
        50%
        31.2
        BMT101D-7_CTCTCTAC-TCTTACGC_S81_L004_R2_001
        56.2%
        50%
        31.2
        BMT101D14_CGTACTAG-TATGCAGT_S78_L004_R1_001
        46.3%
        47%
        28.9
        BMT101D14_CGTACTAG-TATGCAGT_S78_L004_R2_001
        45.8%
        46%
        28.9
        BMT101D1_AAGAGGCA-TCGCATAA_S77_L004_R1_001
        63.0%
        54%
        28.4
        BMT101D1_AAGAGGCA-TCGCATAA_S77_L004_R2_001
        60.6%
        54%
        28.4
        BMT101D30_CTCTCTAC-ATTAGACG_S79_L004_R1_001
        49.1%
        47%
        28.2
        BMT101D30_CTCTCTAC-ATTAGACG_S79_L004_R2_001
        47.9%
        47%
        28.2
        BMT101D7_CTCTCTAC-CTAGTCGA_S80_L004_R1_001
        53.9%
        47%
        30.5
        BMT101D7_CTCTCTAC-CTAGTCGA_S80_L004_R2_001
        52.5%
        46%
        30.5
        BMT102D-9_TAGGCATG-TCGCATAA_S86_L004_R1_001
        26.3%
        48%
        31.0
        BMT102D-9_TAGGCATG-TCGCATAA_S86_L004_R2_001
        24.7%
        47%
        31.0
        BMT102D10_AAGAGGCA-ATTAGACG_S82_L004_R1_001
        32.0%
        45%
        19.7
        BMT102D10_AAGAGGCA-ATTAGACG_S82_L004_R2_001
        31.4%
        45%
        19.7
        BMT102D14_CGAGGCTG-TATGCAGT_S83_L004_R1_001
        33.8%
        45%
        16.7
        BMT102D14_CGAGGCTG-TATGCAGT_S83_L004_R2_001
        31.9%
        45%
        16.7
        BMT102D28_TAGCGCTC-AGAGGATA_S84_L004_R1_001
        38.3%
        45%
        33.9
        BMT102D28_TAGCGCTC-AGAGGATA_S84_L004_R2_001
        37.8%
        45%
        33.9
        BMT102D3_GTAGAGGA-CTAGTCGA_S85_L004_R1_001
        39.8%
        43%
        26.1
        BMT102D3_GTAGAGGA-CTAGTCGA_S85_L004_R2_001
        37.7%
        42%
        26.1
        BMT103D-1_GGACTCCT-TATGCAGT_S87_L004_R1_001
        24.9%
        45%
        26.0
        BMT103D-1_GGACTCCT-TATGCAGT_S87_L004_R2_001
        24.1%
        45%
        26.0
        BMT103D-8_TAGCGCTC-TCGCATAA_S92_L004_R1_001
        24.1%
        47%
        23.5
        BMT103D-8_TAGCGCTC-TCGCATAA_S92_L004_R2_001
        23.4%
        47%
        23.5
        BMT103D14_CGTACTAG-CTAGTCGA_S88_L004_R1_001
        28.3%
        46%
        25.2
        BMT103D14_CGTACTAG-CTAGTCGA_S88_L004_R2_001
        27.4%
        46%
        25.2
        BMT103D24_AGGCAGAA-TCTTACGC_S89_L004_R1_001
        30.0%
        44%
        22.5
        BMT103D24_AGGCAGAA-TCTTACGC_S89_L004_R2_001
        27.2%
        44%
        22.5
        BMT103D27_CGGAGCCT-CTAGTCGA_S90_L004_R1_001
        28.0%
        46%
        36.7
        BMT103D27_CGGAGCCT-CTAGTCGA_S90_L004_R2_001
        27.1%
        45%
        36.7
        BMT103D8_GTAGAGGA-CTCCTTAC_S91_L004_R1_001
        28.0%
        46%
        22.3
        BMT103D8_GTAGAGGA-CTCCTTAC_S91_L004_R2_001
        26.1%
        45%
        22.3
        BMT104D-53_CTCTCTAC-ACTCTAGG_S95_L004_R1_001
        28.7%
        50%
        27.5
        BMT104D-53_CTCTCTAC-ACTCTAGG_S95_L004_R2_001
        29.1%
        50%
        27.5
        BMT104D0_AAGAGGCA-TATGCAGT_S93_L004_R1_001
        32.2%
        48%
        22.3
        BMT104D0_AAGAGGCA-TATGCAGT_S93_L004_R2_001
        30.4%
        47%
        22.3
        BMT104D14_TAGGCATG-AGAGGATA_S94_L004_R1_001
        27.8%
        48%
        24.5
        BMT104D14_TAGGCATG-AGAGGATA_S94_L004_R2_001
        26.7%
        47%
        24.5
        BMT104D24_CGTACTAG-TATGCAGT_S21_L004_R1_001
        29.7%
        48%
        23.7
        BMT104D24_CGTACTAG-TATGCAGT_S21_L004_R2_001
        28.5%
        47%
        23.7
        BMT104D29_TAAGGCGA-CTCCTTAC_S22_L004_R1_001
        17.4%
        48%
        11.4
        BMT104D29_TAAGGCGA-CTCCTTAC_S22_L004_R2_001
        16.5%
        48%
        11.4
        BMT104D7_AGGCAGAA-TCGCATAA_S96_L004_R1_001
        34.7%
        45%
        26.5
        BMT104D7_AGGCAGAA-TCGCATAA_S96_L004_R2_001
        32.3%
        45%
        26.5
        BMT105D-1_AAGAGGCA-AGAGGATA_S97_L004_R1_001
        31.7%
        44%
        29.0
        BMT105D-1_AAGAGGCA-AGAGGATA_S97_L004_R2_001
        31.2%
        43%
        29.0
        BMT105D-8_GCTCATGA-CTAGTCGA_S99_L004_R1_001
        22.5%
        45%
        22.0
        BMT105D-8_GCTCATGA-CTAGTCGA_S99_L004_R2_001
        21.8%
        44%
        22.0
        BMT105D7_AAGAGGCA-CTCCTTAC_S98_L004_R1_001
        38.2%
        45%
        26.3
        BMT105D7_AAGAGGCA-CTCCTTAC_S98_L004_R2_001
        37.1%
        44%
        26.3
        BMT106D0_CGGAGCCT-TCTTACGC_S23_L004_R1_001
        33.8%
        46%
        24.7
        BMT106D0_CGGAGCCT-TCTTACGC_S23_L004_R2_001
        33.2%
        45%
        24.7
        BMT106D14_AGGCAGAA-TCTTACGC_S24_L004_R1_001
        21.6%
        47%
        18.9
        BMT106D14_AGGCAGAA-TCTTACGC_S24_L004_R2_001
        19.1%
        46%
        18.9
        BMT106PRE_CGTACTAG-TCTTACGC_S100_L004_R1_001
        17.6%
        50%
        22.5
        BMT106PRE_CGTACTAG-TCTTACGC_S100_L004_R2_001
        17.5%
        50%
        22.5
        BMT108D-33_CGTACTAG-ATTAGACG_S26_L004_R1_001
        13.5%
        48%
        18.4
        BMT108D-33_CGTACTAG-ATTAGACG_S26_L004_R2_001
        13.7%
        47%
        18.4
        BMT108D0_CTCTCTAC-TATGCAGT_S25_L004_R1_001
        29.5%
        50%
        24.7
        BMT108D0_CTCTCTAC-TATGCAGT_S25_L004_R2_001
        27.5%
        50%
        24.7
        BMT108PRE_TAGGCATG-TATGCAGT_S101_L004_R1_001
        19.3%
        47%
        23.4
        BMT108PRE_TAGGCATG-TATGCAGT_S101_L004_R2_001
        18.2%
        47%
        23.4
        BMT109D-6_CGAGGCTG-TCTTACGC_S102_L004_R1_001
        19.7%
        47%
        18.2
        BMT109D-6_CGAGGCTG-TCTTACGC_S102_L004_R2_001
        18.2%
        46%
        18.2
        BMT109D0_CGGAGCCT-TATGCAGT_S22_L003_R1_001
        37.9%
        45%
        31.8
        BMT109D0_CGGAGCCT-TATGCAGT_S22_L003_R2_001
        35.8%
        44%
        31.8
        BMT109D14_TAGCGCTC-TCGCATAA_S27_L004_R1_001
        21.5%
        45%
        17.5
        BMT109D14_TAGCGCTC-TCGCATAA_S27_L004_R2_001
        21.3%
        45%
        17.5
        BMT109d29_CGAGGCTG-TCGCATAA_S28_L004_R1_001
        12.8%
        47%
        12.3
        BMT109d29_CGAGGCTG-TCGCATAA_S28_L004_R2_001
        12.3%
        46%
        12.3
        BMT110D-9_AGGCAGAA-CTAGTCGA_S32_L004_R1_001
        25.0%
        44%
        17.3
        BMT110D-9_AGGCAGAA-CTAGTCGA_S32_L004_R2_001
        23.6%
        43%
        17.3
        BMT110D15_CGAGGCTG-ACTCTAGG_S29_L004_R1_001
        25.8%
        49%
        22.1
        BMT110D15_CGAGGCTG-ACTCTAGG_S29_L004_R2_001
        26.6%
        47%
        22.1
        BMT110D24_TAGCGCTC-AGAGGATA_S30_L004_R1_001
        31.9%
        45%
        24.1
        BMT110D24_TAGCGCTC-AGAGGATA_S30_L004_R2_001
        30.9%
        44%
        24.1
        BMT110D4_CGAGGCTG-CTCCTTAC_S31_L004_R1_001
        35.7%
        45%
        22.2
        BMT110D4_CGAGGCTG-CTCCTTAC_S31_L004_R2_001
        35.3%
        45%
        22.2
        BMT111D-8_CGAGGCTG-AGAGGATA_S36_L004_R1_001
        21.4%
        46%
        22.7
        BMT111D-8_CGAGGCTG-AGAGGATA_S36_L004_R2_001
        21.7%
        45%
        22.7
        BMT111D21_GCTCATGA-ACTCTAGG_S33_L004_R1_001
        22.2%
        48%
        19.0
        BMT111D21_GCTCATGA-ACTCTAGG_S33_L004_R2_001
        21.1%
        47%
        19.0
        BMT111D3_GTAGAGGA-ACTCTAGG_S34_L004_R1_001
        27.1%
        45%
        29.8
        BMT111D3_GTAGAGGA-ACTCTAGG_S34_L004_R2_001
        26.4%
        44%
        29.8
        BMT111D6_TAGCGCTC-CTCCTTAC_S35_L004_R1_001
        26.3%
        46%
        20.7
        BMT111D6_TAGCGCTC-CTCCTTAC_S35_L004_R2_001
        26.4%
        45%
        20.7
        BMT112D-6_AGGCAGAA-CTCCTTAC_S39_L004_R1_001
        27.3%
        44%
        32.1
        BMT112D-6_AGGCAGAA-CTCCTTAC_S39_L004_R2_001
        25.7%
        43%
        32.1
        BMT112D15_GGACTCCT-CTCCTTAC_S37_L004_R1_001
        30.1%
        49%
        39.4
        BMT112D15_GGACTCCT-CTCCTTAC_S37_L004_R2_001
        28.9%
        48%
        39.4
        BMT112D19_AGGCAGAA-ACTCTAGG_S38_L004_R1_001
        17.5%
        46%
        19.2
        BMT112D19_AGGCAGAA-ACTCTAGG_S38_L004_R2_001
        16.3%
        46%
        19.2
        BMT112D7_CTCTCTAC-ATTAGACG_S40_L004_R1_001
        36.4%
        49%
        17.8
        BMT112D7_CTCTCTAC-ATTAGACG_S40_L004_R2_001
        35.2%
        48%
        17.8
        BMT113D-12_TAGGCATG-TCTTACGC_S41_L004_R1_001
        27.2%
        52%
        17.0
        BMT113D-12_TAGGCATG-TCTTACGC_S41_L004_R2_001
        23.1%
        51%
        17.0
        BMT114D-36_TAGGCATG-CTCCTTAC_S42_L004_R1_001
        41.6%
        45%
        18.3
        BMT114D-36_TAGGCATG-CTCCTTAC_S42_L004_R2_001
        37.9%
        44%
        18.3
        BMT114D25_AGGCAGAA-CTAGTCGA_S23_L003_R1_001
        59.3%
        43%
        20.4
        BMT114D25_AGGCAGAA-CTAGTCGA_S23_L003_R2_001
        53.2%
        43%
        20.4
        BMT114D28_CTCTCTAC-TCGCATAA_S24_L003_R1_001
        62.6%
        46%
        18.0
        BMT114D28_CTCTCTAC-TCGCATAA_S24_L003_R2_001
        58.5%
        46%
        18.0
        BMT115D18_GTAGAGGA-ATTAGACG_S25_L003_R1_001
        27.8%
        45%
        24.9
        BMT115D18_GTAGAGGA-ATTAGACG_S25_L003_R2_001
        26.4%
        45%
        24.9
        BMT115pre_CGTACTAG-CTCCTTAC_S43_L004_R1_001
        25.3%
        44%
        23.6
        BMT115pre_CGTACTAG-CTCCTTAC_S43_L004_R2_001
        24.1%
        44%
        23.6
        BMT116D-3_TAGGCATG-TATGCAGT_S45_L004_R1_001
        20.5%
        44%
        16.4
        BMT116D-3_TAGGCATG-TATGCAGT_S45_L004_R2_001
        19.0%
        44%
        16.4
        BMT116D1_TAAGGCGA-TCTTACGC_S44_L004_R1_001
        19.4%
        48%
        17.1
        BMT116D1_TAAGGCGA-TCTTACGC_S44_L004_R2_001
        16.8%
        47%
        17.1
        BMT118D-9_CGGAGCCT-ACTCTAGG_S48_L004_R1_001
        22.3%
        46%
        23.0
        BMT118D-9_CGGAGCCT-ACTCTAGG_S48_L004_R2_001
        22.6%
        45%
        23.0
        BMT118D10_TAGCGCTC-CTAGTCGA_S46_L004_R1_001
        35.6%
        53%
        16.2
        BMT118D10_TAGCGCTC-CTAGTCGA_S46_L004_R2_001
        34.5%
        53%
        16.2
        BMT118D4_GCTCATGA-TCGCATAA_S47_L004_R1_001
        16.6%
        45%
        17.1
        BMT118D4_GCTCATGA-TCGCATAA_S47_L004_R2_001
        16.3%
        45%
        17.1
        BMT119D-7_AGGCAGAA-TATGCAGT_S50_L004_R1_001
        14.8%
        51%
        15.8
        BMT119D-7_AGGCAGAA-TATGCAGT_S50_L004_R2_001
        11.9%
        51%
        15.8
        BMT119D1_AGGCAGAA-TCGCATAA_S49_L004_R1_001
        14.0%
        48%
        26.9
        BMT119D1_AGGCAGAA-TCGCATAA_S49_L004_R2_001
        13.4%
        47%
        26.9
        BMT119D9_GCTCATGA-CTAGTCGA_S51_L004_R1_001
        37.2%
        45%
        17.6
        BMT119D9_GCTCATGA-CTAGTCGA_S51_L004_R2_001
        36.5%
        44%
        17.6
        BMT120D-5_CGTACTAG-ACTCTAGG_S53_L004_R1_001
        12.3%
        44%
        7.1
        BMT120D-5_CGTACTAG-ACTCTAGG_S53_L004_R2_001
        11.8%
        44%
        7.1
        BMT120D0_TAGCGCTC-TATGCAGT_S52_L004_R1_001
        24.4%
        45%
        30.4
        BMT120D0_TAGCGCTC-TATGCAGT_S52_L004_R2_001
        23.9%
        44%
        30.4
        BMT120D23_CGTACTAG-TCGCATAA_S26_L003_R1_001
        35.5%
        47%
        16.8
        BMT120D23_CGTACTAG-TCGCATAA_S26_L003_R2_001
        32.7%
        46%
        16.8
        BMT120D6_CTCTCTAC-TCTTACGC_S54_L004_R1_001
        35.6%
        43%
        24.6
        BMT120D6_CTCTCTAC-TCTTACGC_S54_L004_R2_001
        35.5%
        43%
        24.6
        BMT121D-6_CGGAGCCT-AGAGGATA_S57_L004_R1_001
        22.8%
        45%
        22.4
        BMT121D-6_CGGAGCCT-AGAGGATA_S57_L004_R2_001
        22.6%
        44%
        22.4
        BMT121D0_CGAGGCTG-ATTAGACG_S55_L004_R1_001
        29.0%
        44%
        16.3
        BMT121D0_CGAGGCTG-ATTAGACG_S55_L004_R2_001
        28.9%
        44%
        16.3
        BMT121D15_AGGCAGAA-ACTCTAGG_S27_L003_R1_001
        42.1%
        47%
        34.7
        BMT121D15_AGGCAGAA-ACTCTAGG_S27_L003_R2_001
        40.0%
        47%
        34.7
        BMT121D22_TAGCGCTC-ATTAGACG_S56_L004_R1_001
        26.5%
        46%
        19.6
        BMT121D22_TAGCGCTC-ATTAGACG_S56_L004_R2_001
        26.4%
        46%
        19.6
        BMT121D26_AAGAGGCA-TCTTACGC_S28_L003_R1_001
        36.0%
        47%
        16.5
        BMT121D26_AAGAGGCA-TCTTACGC_S28_L003_R2_001
        34.0%
        47%
        16.5
        BMT123D-8_CGGAGCCT-CTCCTTAC_S58_L004_R1_001
        7.9%
        49%
        6.5
        BMT123D-8_CGGAGCCT-CTCCTTAC_S58_L004_R2_001
        7.7%
        48%
        6.5
        BMT123D0_GCTCATGA-CTAGTCGA_S29_L003_R1_001
        38.4%
        48%
        27.7
        BMT123D0_GCTCATGA-CTAGTCGA_S29_L003_R2_001
        36.0%
        48%
        27.7
        BMT124D-13_GGACTCCT-TATGCAGT_S60_L004_R1_001
        18.1%
        47%
        30.5
        BMT124D-13_GGACTCCT-TATGCAGT_S60_L004_R2_001
        17.7%
        47%
        30.5
        BMT124D0_CGAGGCTG-CTAGTCGA_S59_L004_R1_001
        19.0%
        49%
        19.0
        BMT124D0_CGAGGCTG-CTAGTCGA_S59_L004_R2_001
        19.0%
        48%
        19.0
        BMT124D17_CGAGGCTG-CTAGTCGA_S30_L003_R1_001
        20.3%
        47%
        15.0
        BMT124D17_CGAGGCTG-CTAGTCGA_S30_L003_R2_001
        19.0%
        46%
        15.0
        BMT124D7_GGACTCCT-CTAGTCGA_S61_L004_R1_001
        28.2%
        44%
        18.6
        BMT124D7_GGACTCCT-CTAGTCGA_S61_L004_R2_001
        27.1%
        44%
        18.6
        BMT125D-14_CTCTCTAC-CTCCTTAC_S62_L004_R1_001
        16.4%
        46%
        14.7
        BMT125D-14_CTCTCTAC-CTCCTTAC_S62_L004_R2_001
        13.7%
        46%
        14.7
        BMT125D0_TAGCGCTC-ATTAGACG_S31_L003_R1_001
        18.2%
        48%
        20.3
        BMT125D0_TAGCGCTC-ATTAGACG_S31_L003_R2_001
        17.7%
        47%
        20.3
        BMT125D21_GGACTCCT-TCGCATAA_S32_L003_R1_001
        34.0%
        45%
        38.5
        BMT125D21_GGACTCCT-TCGCATAA_S32_L003_R2_001
        32.4%
        45%
        38.5
        BMT125D7_CGAGGCTG-TATGCAGT_S33_L003_R1_001
        13.1%
        48%
        12.1
        BMT125D7_CGAGGCTG-TATGCAGT_S33_L003_R2_001
        11.9%
        47%
        12.1
        BMT126D-12_GTAGAGGA-CTCCTTAC_S34_L003_R1_001
        53.3%
        44%
        93.4
        BMT126D-12_GTAGAGGA-CTCCTTAC_S34_L003_R2_001
        49.7%
        44%
        93.4
        BMT126D21_CTCTCTAC-ATTAGACG_S35_L003_R1_001
        39.5%
        45%
        34.2
        BMT126D21_CTCTCTAC-ATTAGACG_S35_L003_R2_001
        38.4%
        44%
        34.2
        BMT126D8_TAAGGCGA-CTAGTCGA_S64_L004_R1_001
        26.6%
        45%
        19.5
        BMT126D8_TAAGGCGA-CTAGTCGA_S64_L004_R2_001
        25.9%
        44%
        19.5
        BMT126d1_GTAGAGGA-AGAGGATA_S63_L004_R1_001
        25.6%
        47%
        18.6
        BMT126d1_GTAGAGGA-AGAGGATA_S63_L004_R2_001
        24.3%
        46%
        18.6
        BMT127D-13_GGACTCCT-ACTCTAGG_S36_L003_R1_001
        33.2%
        46%
        36.3
        BMT127D-13_GGACTCCT-ACTCTAGG_S36_L003_R2_001
        30.7%
        46%
        36.3
        BMT127D1_AGGCAGAA-ATTAGACG_S65_L004_R1_001
        28.2%
        45%
        16.4
        BMT127D1_AGGCAGAA-ATTAGACG_S65_L004_R2_001
        26.4%
        45%
        16.4
        BMT127D21_CGAGGCTG-AGAGGATA_S37_L003_R1_001
        52.5%
        46%
        41.5
        BMT127D21_CGAGGCTG-AGAGGATA_S37_L003_R2_001
        52.3%
        44%
        41.5
        BMT127D6_TAGGCATG-AGAGGATA_S38_L003_R1_001
        40.1%
        49%
        33.8
        BMT127D6_TAGGCATG-AGAGGATA_S38_L003_R2_001
        38.3%
        48%
        33.8
        BMT128D-14_TAAGGCGA-AGAGGATA_S39_L003_R1_001
        33.8%
        46%
        40.8
        BMT128D-14_TAAGGCGA-AGAGGATA_S39_L003_R2_001
        31.9%
        46%
        40.8
        BMT129D-6_GTAGAGGA-ACTCTAGG_S42_L003_R1_001
        21.0%
        48%
        27.3
        BMT129D-6_GTAGAGGA-ACTCTAGG_S42_L003_R2_001
        19.3%
        47%
        27.3
        BMT129D0_TAGGCATG-ATTAGACG_S40_L003_R1_001
        25.5%
        47%
        40.3
        BMT129D0_TAGGCATG-ATTAGACG_S40_L003_R2_001
        25.2%
        46%
        40.3
        BMT129D15_TAGCGCTC-TCTTACGC_S41_L003_R1_001
        19.9%
        47%
        23.2
        BMT129D15_TAGCGCTC-TCTTACGC_S41_L003_R2_001
        19.7%
        47%
        23.2
        BMT129D23_TAGGCATG-CTAGTCGA_S66_L004_R1_001
        20.9%
        46%
        19.5
        BMT129D23_TAGGCATG-CTAGTCGA_S66_L004_R2_001
        18.6%
        46%
        19.5
        BMT129D28_CTCTCTAC-TCGCATAA_S67_L004_R1_001
        17.0%
        46%
        19.3
        BMT129D28_CTCTCTAC-TCGCATAA_S67_L004_R2_001
        17.0%
        45%
        19.3
        BMT130D-4_TAAGGCGA-TCTTACGC_S46_L003_R1_001
        39.4%
        44%
        21.6
        BMT130D-4_TAAGGCGA-TCTTACGC_S46_L003_R2_001
        35.8%
        44%
        21.6
        BMT130D0_TAAGGCGA-TCGCATAA_S43_L003_R1_001
        22.7%
        47%
        33.5
        BMT130D0_TAAGGCGA-TCGCATAA_S43_L003_R2_001
        21.4%
        46%
        33.5
        BMT130D20_CTCTCTAC-TATGCAGT_S44_L003_R1_001
        22.6%
        45%
        17.8
        BMT130D20_CTCTCTAC-TATGCAGT_S44_L003_R2_001
        21.3%
        44%
        17.8
        BMT130D25_CGTACTAG-ACTCTAGG_S45_L003_R1_001
        25.1%
        47%
        29.2
        BMT130D25_CGTACTAG-ACTCTAGG_S45_L003_R2_001
        24.7%
        46%
        29.2
        BMT130D7_CGAGGCTG-TCGCATAA_S47_L003_R1_001
        30.6%
        44%
        25.9
        BMT130D7_CGAGGCTG-TCGCATAA_S47_L003_R2_001
        28.5%
        43%
        25.9
        BMT131D-6_CTCTCTAC-TCTTACGC_S51_L003_R1_001
        21.6%
        47%
        18.8
        BMT131D-6_CTCTCTAC-TCTTACGC_S51_L003_R2_001
        20.2%
        47%
        18.8
        BMT131D0_AAGAGGCA-AGAGGATA_S48_L003_R1_001
        23.2%
        49%
        35.9
        BMT131D0_AAGAGGCA-AGAGGATA_S48_L003_R2_001
        21.6%
        49%
        35.9
        BMT131D14_CGGAGCCT-TCGCATAA_S49_L003_R1_001
        20.0%
        49%
        21.7
        BMT131D14_CGGAGCCT-TCGCATAA_S49_L003_R2_001
        19.5%
        48%
        21.7
        BMT131D22_CTCTCTAC-CTAGTCGA_S50_L003_R1_001
        27.6%
        47%
        18.5
        BMT131D22_CTCTCTAC-CTAGTCGA_S50_L003_R2_001
        26.7%
        46%
        18.5
        BMT131D7_CGTACTAG-ATTAGACG_S52_L003_R1_001
        20.3%
        48%
        22.2
        BMT131D7_CGTACTAG-ATTAGACG_S52_L003_R2_001
        19.8%
        47%
        22.2
        BMT132D3_AAGAGGCA-CTAGTCGA_S53_L003_R1_001
        23.4%
        43%
        18.8
        BMT132D3_AAGAGGCA-CTAGTCGA_S53_L003_R2_001
        22.9%
        43%
        18.8
        BMT133D-6_GTAGAGGA-TCTTACGC_S57_L003_R1_001
        32.7%
        43%
        16.6
        BMT133D-6_GTAGAGGA-TCTTACGC_S57_L003_R2_001
        30.5%
        43%
        16.6
        BMT133D15_GGACTCCT-CTCCTTAC_S55_L003_R1_001
        36.8%
        46%
        25.3
        BMT133D15_GGACTCCT-CTCCTTAC_S55_L003_R2_001
        35.2%
        46%
        25.3
        BMT133D1_TAGGCATG-ACTCTAGG_S54_L003_R1_001
        43.1%
        45%
        30.0
        BMT133D1_TAGGCATG-ACTCTAGG_S54_L003_R2_001
        42.0%
        45%
        30.0
        BMT133D26_TAGGCATG-TATGCAGT_S56_L003_R1_001
        32.3%
        44%
        21.8
        BMT133D26_TAGGCATG-TATGCAGT_S56_L003_R2_001
        30.8%
        44%
        21.8
        BMT134D15_AGGCAGAA-TATGCAGT_S58_L003_R1_001
        30.7%
        51%
        35.0
        BMT134D15_AGGCAGAA-TATGCAGT_S58_L003_R2_001
        26.5%
        50%
        35.0
        BMT134D2_CGTACTAG-TCTTACGC_S59_L003_R1_001
        33.3%
        47%
        25.0
        BMT134D2_CGTACTAG-TCTTACGC_S59_L003_R2_001
        31.7%
        47%
        25.0
        BMT134D8_GCTCATGA-AGAGGATA_S60_L003_R1_001
        45.0%
        51%
        33.2
        BMT134D8_GCTCATGA-AGAGGATA_S60_L003_R2_001
        43.0%
        51%
        33.2
        BMT134pre_AAGAGGCA-ACTCTAGG_S61_L003_R1_001
        26.1%
        47%
        32.8
        BMT134pre_AAGAGGCA-ACTCTAGG_S61_L003_R2_001
        24.8%
        47%
        32.8
        BMT138D5_TAGGCATG-TCTTACGC_S62_L003_R1_001
        21.0%
        47%
        24.3
        BMT138D5_TAGGCATG-TCTTACGC_S62_L003_R2_001
        18.9%
        47%
        24.3
        BMT138pre_TAGCGCTC-AGAGGATA_S63_L003_R1_001
        34.0%
        45%
        47.2
        BMT138pre_TAGCGCTC-AGAGGATA_S63_L003_R2_001
        33.1%
        44%
        47.2
        BMT140D13_AAGAGGCA-TATGCAGT_S64_L003_R1_001
        55.2%
        41%
        13.4
        BMT140D13_AAGAGGCA-TATGCAGT_S64_L003_R2_001
        53.8%
        41%
        13.4
        BMT140D14_TAAGGCGA-ACTCTAGG_S65_L003_R1_001
        47.3%
        46%
        39.7
        BMT140D14_TAAGGCGA-ACTCTAGG_S65_L003_R2_001
        46.2%
        45%
        39.7
        BMT140D62_AGGCAGAA-TCTTACGC_S66_L003_R1_001
        46.3%
        51%
        26.4
        BMT140D62_AGGCAGAA-TCTTACGC_S66_L003_R2_001
        41.4%
        51%
        26.4
        BMT140D75_TAGGCATG-TCGCATAA_S67_L003_R1_001
        45.4%
        49%
        41.2
        BMT140D75_TAGGCATG-TCGCATAA_S67_L003_R2_001
        41.9%
        49%
        41.2
        BMT140pre_CGGAGCCT-ACTCTAGG_S68_L003_R1_001
        35.1%
        45%
        45.9
        BMT140pre_CGGAGCCT-ACTCTAGG_S68_L003_R2_001
        34.3%
        44%
        45.9
        BMT141pre_GCTCATGA-TATGCAGT_S69_L003_R1_001
        24.3%
        48%
        25.8
        BMT141pre_GCTCATGA-TATGCAGT_S69_L003_R2_001
        23.4%
        47%
        25.8
        BMT142D8_GTAGAGGA-TATGCAGT_S70_L003_R1_001
        38.8%
        44%
        23.8
        BMT142D8_GTAGAGGA-TATGCAGT_S70_L003_R2_001
        36.8%
        43%
        23.8
        BMT142pre_CGGAGCCT-CTCCTTAC_S71_L003_R1_001
        39.7%
        45%
        31.2
        BMT142pre_CGGAGCCT-CTCCTTAC_S71_L003_R2_001
        38.1%
        45%
        31.2
        BMT146D2_GGACTCCT-CTAGTCGA_S72_L003_R1_001
        27.5%
        44%
        18.3
        BMT146D2_GGACTCCT-CTAGTCGA_S72_L003_R2_001
        25.7%
        43%
        18.3
        BMT146D42_AAGAGGCA-TCGCATAA_S73_L003_R1_001
        43.2%
        47%
        18.9
        BMT146D42_AAGAGGCA-TCGCATAA_S73_L003_R2_001
        40.2%
        46%
        18.9
        BMT146D52_TAAGGCGA-TATGCAGT_S74_L003_R1_001
        18.2%
        43%
        6.9
        BMT146D52_TAAGGCGA-TATGCAGT_S74_L003_R2_001
        17.5%
        43%
        6.9
        BMT146pre_GTAGAGGA-TCGCATAA_S75_L003_R1_001
        29.9%
        44%
        17.7
        BMT146pre_GTAGAGGA-TCGCATAA_S75_L003_R2_001
        28.1%
        44%
        17.7
        BMT149D12_TAGGCATG-CTAGTCGA_S76_L003_R1_001
        39.6%
        45%
        18.9
        BMT149D12_TAGGCATG-CTAGTCGA_S76_L003_R2_001
        36.2%
        45%
        18.9
        BMT149D17_AAGAGGCA-CTCCTTAC_S77_L003_R1_001
        62.6%
        35%
        19.0
        BMT149D17_AAGAGGCA-CTCCTTAC_S77_L003_R2_001
        56.5%
        35%
        19.0
        BMT149D24_CGTACTAG-CTCCTTAC_S78_L003_R1_001
        50.7%
        45%
        24.0
        BMT149D24_CGTACTAG-CTCCTTAC_S78_L003_R2_001
        48.4%
        45%
        24.0
        BMT149pre_CGGAGCCT-AGAGGATA_S79_L003_R1_001
        56.2%
        42%
        31.6
        BMT149pre_CGGAGCCT-AGAGGATA_S79_L003_R2_001
        52.4%
        40%
        31.6
        BMT151D1_GCTCATGA-TCGCATAA_S80_L003_R1_001
        40.4%
        42%
        19.1
        BMT151D1_GCTCATGA-TCGCATAA_S80_L003_R2_001
        40.2%
        41%
        19.1
        BMT151pre_GCTCATGA-TCTTACGC_S81_L003_R1_001
        20.1%
        46%
        15.8
        BMT151pre_GCTCATGA-TCTTACGC_S81_L003_R2_001
        19.6%
        45%
        15.8
        BMT152PRE_GGACTCCT-ATTAGACG_S82_L003_R1_001
        29.9%
        45%
        14.6
        BMT152PRE_GGACTCCT-ATTAGACG_S82_L003_R2_001
        30.9%
        45%
        14.6
        BMT153pre_GGACTCCT-AGAGGATA_S83_L003_R1_001
        32.3%
        45%
        38.4
        BMT153pre_GGACTCCT-AGAGGATA_S83_L003_R2_001
        31.4%
        45%
        38.4

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (151bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        270 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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